Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2

Influenza A Virus in Swine Surveillance

Fiscal Year 2022 Quarterly Report

Surveillance Summary for Second Quarter Fiscal Year 2022: January 1

to March 31, 2022

Report Summary1

• This report covers the second quarter (Q2) of fiscal year (FY) 2022 from January 1 through 

March 31, 2022.

• In Q2 of FY2022, there were 1,023 samples submitted for influenza A virus (IAV) surveillance in 

swine from 938 accessions. 

• H1N1 was the predominant subtype reported in USDA data in Q2 FY2022.

• Over the past 8 quarters, H1N1 was the predominant subtype in all regions except region 3, 

which H3N2 was the most predominant subtype.

• The Agricultural Research Service (ARS) characterized 197 isolates with published sequences in 

GenBank by phylogenetic analysis for the Q2 FY2022 report

• In Q2 FY2022, the NVSL Diagnostic Virology Laboratory (NVSL) provided 114 isolates to one

academic institution, four government entities, and four pharmaceutical requestors. NVSL 

received 214 isolates into the repository in Q2 FY2022.

Key Points

• Where relevant, the report also includes previous years’ data for historical perspective. 

• The report provides data from both national and regional levels.

• Limited accessions from a region can skew data and lead to misinterpretation. Therefore, less 

inference can be applied to results from Regions 3, 4, and 5.

• All IAV-S submissions are voluntary and based on clinical case submissions to veterinary 

diagnostic labs. These data are not a statistically representative sampling of the U.S. swine 

population.

• Due to the voluntary nature of this surveillance, the information in this report cannot be used to 

determine regional and/or national incidence, prevalence, or other epidemiological measures, 

but it may help identify IAV-S trends. 

Introduction

This report, based on data received into the database as of June 28, 2022, provides a brief update on the 

status of national surveillance for IAV in swine for producers, swine practitioners, diagnosticians and the 

1 In November 2016, VS modernized the process that prepares and stages laboratory results data for reporting. Consequently, 

VS recognizes there is a small difference in previously reported summary numbers for IAV-S surveillance. The results in this 

report reflect updated and corrected numbers achieved with the modernized data process.

Animal and 

Plant Health 

Inspection 

Service

Veterinary 

Services

June 2022
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2 

public. Summaries in this report may differ from those provided in past reports due to the regular 

addition of data from participating laboratories. Reporting months are based on the month the sample 

was collected. The IAV-S surveillance program is voluntary and, as a result, the accessions and samples 

submitted represent a subset of the swine population. Submitted samples should only be collected from 

animals displaying influenza-like illness. When the submitter does not report relevant information, data 

are recorded as “unknown.” Due to its voluntary nature, this surveillance system is not representative of

the total U.S. domestic swine population. Therefore, the data cannot be used to determine IAV-S 

prevalence or other epidemiologic measures in the swine population. However, the data may help 

identify influenza trends in swine. 

A laboratory accession generally represents a set of samples collected at a single premises on a single 

day and received at the laboratory. While a nasal swab or lung tissue sample represents a single animal 

within the herd, a single oral fluid sample may represent one to two pens of animals in a herd. A positive 

sample status is based on the screening real-time reverse transcriptase polymerase chain reaction (rRTPCR) on one or more samples within the accession. The subtype result is based on rRT-PCR-based 

subtyping assays. Virus isolation (VI) and sequencing in the National Animal Health Laboratory Network 

(NAHLN) labs are only attempted on rRT-PCR positives meeting criteria, with sequences deposited into 

GenBank, the public sequence database. On a monthly basis, USDA NVSL also performs whole genomic 

sequencing (WGS) on a selected subset of virus isolates received into the repository through the 

surveillance program and deposits those sequences into Genbank. On a quarterly basis, a phylogenetic 

analysis is performed by USDA’s Agricultural Research Service (ARS) National Animal Disease Center 

(NADC) influenza researchers; phylogenetic analyses are based on all successful USDA surveillance 

sequencing results deposited into GenBank, the public sequence database. 

Program Updates 

Information on IAV-S and the IAV-S surveillance program, as well as previous IAV-S quarterly reports, are 

found at: 

https://www.aphis.usda.gov/aphis/ourfocus/animalhealth/animal-disease-information/swine-diseaseinformation/influenza-a-virus

The focus of IAV-S surveillance remains on acquiring and analyzing contemporary viruses from sick swine 

for ongoing genetic studies. The NAHLN has several submission options to ensure that unusual viruses 

identified by methods other than standardized NAHLN testing processes can be submitted into the 

program. An updated version of the IAV-S NAHLN testing guidelines and instruction sheet can be found 

at:

• Algorithm: 

https://www.aphis.usda.gov/animal_health/animal_dis_spec/swine/downloads/appendix_c_tes

ting_guidelines.pdf

• Instructions: 

https://www-author.aphis.usda.gov/animal_health/animal_dis_spec/swine/downloads/iav-salgorithm-instructions.pdf 

IAV-S isolates can be requested from the NVSL repository by following the instructions found at:

• Isolate request:

https://www.aphis.usda.gov/animal_health/lab_info_services/downloads/OrderingIAVSRepositoryIsolates.pdf
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2 

IAV-S Surveillance Objectives

USDA’s National Surveillance Plan for Swine Influenza Virus in Pigs (July 2010) describes the current 

surveillance system for IAV in swine in detail. The surveillance objectives are to: 

1. Monitor genetic evolution of endemic IAV in swine to better understand endemic and emerging 

influenza virus ecology; 

2. Make influenza isolates from swine available for research and establish a data management system to 

facilitate genetic analysis of these isolates and related information; and 

3. Select proper isolates for the development of relevant diagnostic reagents, updated diagnostic assays, 

and vaccine seed stock products. 

Objective 1. Monitoring Genetic Evolution of Endemic IAV in Swine to 

Better Understand Endemic and Emerging Influenza Virus Ecology

Objective 1 is met through the submission of diagnostic laboratory samples to the surveillance system, 

collection of the viruses that are isolated from the samples, and analysis of the hemagglutinin (HA) and 

neuraminidase (NA) sequences that are generated at the NAHLN laboratories. Each month, selected

viruses undergo whole genome sequencing by the NVSL. Phylogenic analysis of the genetic sequences 

submitted through the surveillance program is provided through an interagency agreement with the 

USDA’s Agricultural Research Service (ARS) National Animal Disease Center (NADC). 

National Surveillance Data Summary

From FY2010 through FY2015, the total number of accessions and samples submitted increased. 

Changes initiated in the program in FY2016 resulted in decreased laboratory accessions and samples, 

however yielded higher percentage of accessions resulting in a virus isolate that could be sequenced and 

analyzed. Based on historical data for successful virus isolation, cycle threshold (Ct) maximum values for 

different sample types were established to try to improve the efficiency of the surveillance program 

while reducing the required resources. If lung/nasal samples have a Ct value of 25 or less and oral fluid 

samples have a Ct value of 20 or less, virus isolation and sequencing will be attempted. If there is 

something unique related to the virus, like it is causing high mortality, but the samples have higher than 

the established maximum Ct values, they will still enter the surveillance stream. 

Through Q2 of FY2022, a total of 1,023 samples were tested from 938 accessions in FY2022 (Figure 1). 

Figure 2 shows the overall trends in rRT-PCR and VI positive accessions and subtyped accessions. 

 

 Figure 1. Number of IAV laboratory accessions and samples tested in swine FY2018 through Q2 FY2022 
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2

Figure 2. Subtyped accessions, rRT-PCR positive accessions, and virus isolation positive accessions over time with trend lines 

for IAV-S, FY2018 through Q2 FY2022

Figure 3 shows the number and distirbution of subtype detections in Q2 FY2022. A total of 202 samples 

were subtyped, including H1N1 (n=90), H1N2 (n=52), H3N2 (n=58), H3N1 (n=0), and mixed (n=2).

Figure 3. Number of IAV-S subtype detections in Q2 FY2022

Figure 4 breaks down accessions by rRT-PCR subtype for FY2018 through Q2 FY2022. H1N1 was the 

predominant subtype detected in 2018, 2020, 2021 and through Q2 FY2022. H1N2 was detected most 

often in 2019. It is important to note that there is wide genetic diversity within each subtype.
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2

Figure 4. Breakdown of accessions by subtype rRT-PCR from FY2018 through Q2 FY2022

Figure 5 displays the number of times VI was attempted in blue, the number of successful VI attempts in 

purple, and the number of sequenced viral isolates submitted to GenBank in green. Since the 

implementation of the June 2016 program modifications, almost all VIs attempted now yield a virus with 

the sequences submitted to Genbank for analysis.

Laboratory accessions were evaluated by age-class for the second quarter. The most common subtype 

isolated among all classes was H1N1 (Table 1). After excluding specimen types that comprised less than 

10 percent of total sample submissions, samples taken from lung tissue were the most successful at 

providing positive virus isolation and submission to GenBank (Table 2).

Figure 5. Number of virus isolations attempted, positive virus isolations, and GenBank submissions from FY2018 through Q2

FY2022
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2 

Table 1. Number of positive accessions tested for IAV-S by age class and viral subtype, Q2 FY2022 

Age Class (group) Number of 

H1N1

Number of 

H1N2

Number of 

H3N1

Number of 

H3N2

Number of 

Mixed

Suckling 28 21 0 20 0 

Nursery 34 20 0 23 0 

Grow/Finish 18 7 0 1 1 

Sow/Boar 3 0 0 0 0 

Not Recorded/Unknown 7 4 0 4 1 

Table 2. Number of positive accessions* tested for IAV-S by specimen type and by viral subtype, Q2 FY2022 

Specimen 

Type 

(group)

Number of 

accessions 

with 

subtype 

reported

Percent of 

subtyped 

accessions 

with 

positive 

virus 

isolation

Number 

of H1N1

Number 

of H1N2

Number 

of H3N1

Number 

of H3N2

Number 

of 

Mixed

Number of 

samples 

sequenced 

and sent to 

GenBank

Lung 185 93% 77 51 0 55 2 171

Nasal or 

Nasal Swab

16 81% 12 1 0 3 0 13

Oral Fluids 0 NA 0 0 0 0 0 0

Other 

Specimens

1 100% 1 0 0 0 0 1

*Accessions may include samples with multiple specimen types. In these cases, individual accessions are counted in more than one specimen 

type category. 

Regional surveillance data

In this section, we present data across five different regions (Figure 6). These regions are based on 

former USDA administrative districts only and do not represent specific industry distributions. 

Submissions are voluntary, as is providing any identifying information beyond State of animal origin with 

the submission. Therefore, regional and/or national incidence, prevalence, or other epidemiological 

measures cannot be determined from this data.

Figure 6. A map of the regions for national IAV-S surveillance
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2 

Summary of Regional Data from ARS

Table 3 lists the most predominant HA/NA phylo-type pairs by region from April 2021-March 2022, with 

predominant being defined as comprising at least 10% of a region’s HA/NA pairs. The total number 

column displays the total number of isolates that were phylo-typed for each region from April 2021-

March 2022. 

Figure 7. Distribution of rRT-PCR subtyped accessions across the five regions for Q2 FY2020 through Q2 FY2022 

Table 3. Summary of predominant HA/NA* phylo-types by region in a 1-year window from April 2021 through 

March 2022

 Region Total number Predominant HA/NA subtypes

1 77 H3N2 (H3-Cluster IV-A / N2-2002B) (n=31)

H1N2 (H1-Delta2 / N2-1998B) (n=15)

H1N1 (H1-Alpha / N1-Classical) (n=14)

2+ 525 H1N1 (H1-Gamma / N1-Classical) (n=169)

H1N2 (H1-Delta2 / N2-1998B) (n=99)

H3N2 (H3-Cluster IV-A / N2-2002B) (n=68)

3 49 H3N2 (H3-2010.1 / N2-2002B) (n=9)

H1N1 (H1-Pandemic / N1-Pandemic) (n=6)

H3N2(H3-2010.1 / N2-2002A) (n=6)

4 63 H1N1 (H1-Gamma / N1-Classical) (n=14)

H1N1 (H1-Pandemic / N1-Pandemic) (n=8)

H1N1 (H1-Alpha / N1-2002B (n=8)

5++ 10 H1N1 (H1-Pandemic / N1-Pandemic) (n=4)

H1N2 (H1-Delta2 / N2-199B) (n=2)

H1N1 (H1-Gamma / N1-Classical) (n=1)

All 724 H1N1 (H1-Gamma / N1-Classical) (n=201)

H1N2 (H1-Delta2 / N2-1998B) (n=124)

H3N2 (H3-Cluster IV-A / N2-2002B (n=101)

*HA/NA pairs included if they compromise over 10% from a region

+ Most diversity of all regions

++ Low participation
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2

Figure 7 shows the distribution of rRT-PCR subtyped accessions across the five regions for Q2 FY2020 

through Q2 FY2022. Over the last 8 quarters, H1N1 was the predominant subtype in regions 1, 2, 4, and 

5. In region 3, H3N2 was the most predominant subtype.

Phylogenetic analysis of sequences from the IAV-S surveillance system

Phylogenetic analysis of gene sequences of IAV in swine is conducted to further examine the genetic 

changes that occur in HA, NA, and Matrix (M) genes of this rapidly changing virus. Through collaboration 

with ARS, a dataset2,3 of 197 isolates with published sequences in GenBank was characterized by 

phylogenetic analysis for the Q2 FY2022 report. This analysis provides information on the genetic 

diversity and evolutionary patterns of influenza in swine and allows for inferences about population 

and/or vaccine immunity.

The following series of bar charts parse the data into an approximately 2-year window by quarters and 

region, describing virus subtypes (Figure 8) and phylogenetic clades of H1, H3, N1 and N2 subtypes 

(Figures 9-12). Regional charts depicting the various combinations of HA and NA are available in 

Appendix 1.

Figure 8 demonstrates the four subtypes H1N1, H1N2, H3N1 and H3N2 across the five regions. Regions 1 

and 2 reported the most submissions, with a mixture of mostly H1N1, H1N2, and H3N2 in region 2 and a 

mixture of mostly H1N1 and H3N2 in region 1. Limited accessions from a region can skew data and lead 

to misinterpretation, therefore less inference can be applied to results from regions 3, 4, and 5. 

Figure 8. Temporal distribution of Influenza A virus subtype by region for Q3 FY2020 to Q2 FY2022

National phylogenetic HA gene information 

HA genes from H1 subtype viruses are classified as alpha, beta, gamma, delta-1, delta-2, or pandemic 

H1N1 2009 (H1N1pdm09) phylogenetic clades based on a previously published nomenclature system. 

Similarly, H3 subtype viruses are classified as Cluster IV, Cluster IV-A, Cluster IV-B, Cluster IV-C, Cluster 

IV-D, Cluster IV-E, Cluster IV-F, or human-like. From Q3 FY2020 through Q2 FY2022, H1-Gamma 

remained the predominant H1 HA gene (Figure 9) and H3-Cluster IV-A remained the predominant H3 HA 

gene (Figure 10).

2 Participating NAHLN labs included M gene sequencing in their testing until July 2016 because the 2009 H1N1 M gene was the 

predominant circulating gene. 3 The ARS dataset is comprised of IAV-S surveillance isolate sequences that were posted in Genbank. This represents only a 

subset of the complete IAV-S surveillance dataset that includes PCR diagnostic test-based results as well as sequencing results. 

Therefore, ARS dataset results, such as subtype percentages, differ from the complete IAV-S dataset results provided in other 

sections of this report.
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2

Figure 10. Temporal distribution of H1 phylogenetic clades by region for Q3 FY2020 to Q2 FY2022

National phylogenetic NA gene information

In Q2 FY2022, N1-Classical was the most predominant N1 phylogenetic-clade (Figure 11) and represented 

approximately 88% of the Q2 FY2022 N1 collection.

In Q2 FY2022, the most predominant N2 phylogenetic-clade was 2002B-lineage (Figure 12) and represented 

approximately 55% of the Q2 FY2022 N2 collection.

Figure 11. Temporal distribution of N1 phylogenetic-clades by region for Q3 FY2020 to Q2 FY2022

Figure 9. Temporal distribution of H3 phylogenetic clades by region for Q3 FY2020 to Q2 FY2022
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2

Figure 12. Temporal distribution of N2 phylogenetic-clades by region for Q3 FY2020 to Q2 FY2022

Gene constellations information

The most dominant internal gene constellations for the last year were TTTPPT (54%), TTTTPT (23%) and 

TTPPPT (9%). From April 2020 to December 2021, out of 579 strains with completed whole genomic 

sequencing that were analyzed, 36% were H1N1, 32% were H1N2, 1% H3N1, and 31% were H3N2, with 25 

unique gene constellations and 41 unique HA/NA pairs (Figure 13). Eight percent of observed constellations 

had at least one vaccine gene.

Internal gene constellation in the order of PB2-PB1-PA-NP-M-NS on y-axis

T=TRIG; P=Pandemic; V=Vaccine; H=Human-seasonal

Figure 13. Temporal distribution of N2 phylogenetic-clades by region for Q3 FY2020 to Q2 FY2022

Representative HA genes

Six months of IAV-S data were used by the NADC to identify circulating HA clades. For each circulating HA 

clade, an amino acid alignment for the HA1 was used to generate a majority consensus sequence. NADC 

used genetic distance to the clade consensus to identify the best-matched field strain housed in the USDA 

IAV-S virus repository (Table 4). 
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2 

Table 4. IAV-S Surveillance NADC Representative HA genes*

Strain Global Clade US Clade

A/swine/Illinois/A02524514/2020 1A.1.1 Alpha-del

A/swine/Iowa/A02524480/2020 1A.3.3.2 H1N1pdm09

A/swine/Minnesota/A02635908/2021 1A.3.3.3 Gamma.c3

A/swine/Iowa/A02635863/2021 1B.2.1 Delta-2

A/swine/Wyoming/A02525343/2021 1B.2.2.1 Delta-1a

A/swine/Iowa/A02524534/2020 1B.2.2.2 Delta-1b

A/swine/Iowa/A02635890/2021 1990.4.a C-IV.a

A/swine/Kansas/A02245675/2020 2010.1 2010.1

A/swine/Indiana/A02635878/2021 2010.2 2010.2

*6-month HA1 consensus generated and best-matched field strain in the repository was identified 

Objective 2. Make Influenza Isolates from Swine Available for Research and 

Establish a Data Management System to Facilitate Genetic Analysis of these 

Isolates and Related Information

A primary goal of the IAV swine surveillance program is to share selected virus isolates obtained through 

the surveillance system with public health, animal health, and academic researchers to facilitate genetic 

analysis and research on viruses of interest. The NVSL Diagnostic Virology Laboratory maintains a

repository of the viruses submitted into the surveillance system and provides these viruses upon request. 

In Q2 FY2022, the NVSL Diagnostic Virology Laboratory provided 114 isolates to one academic institution, 

four government entities, and four pharmaceutical requestors. NVSL received 214 isolates into the 

repository in Q2 FY2022. Table 5 reports the total number of virus isolates received into the repository 

each year from FY2014 through Q2 of FY2022. Table 6 reports the total number of isolates by subtype 

available in the repository for sharing. 

Table 5. Virus isolates received in NVSL repository by year 

 Fiscal Year Number of isolates

FY2022 245

FY2021 1,108

FY2020 1,074

FY2019 1,055

FY2018 994

FY2017 844

FY2016 1,046

FY2015 883

FY2014 765

TOTAL TO DATE 8,014

 
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2 

 

Objective 3. Select Proper Isolates for Development of Relevant Diagnostic 

Reagents, Updating Diagnostic Assays, and Vaccine Seed Stock Products

USDA makes IAV-S isolates available in the public domain for further research. ARS-NADC conducts 

research on isolates obtained from the repository and sequences generated from the surveillance system. 

Genetic sequencing from the USDA program that is reported to GenBank is available for private 

corporations, government entities, academia, and other scientific community partners for research and 

vaccine strain selection and efficacy testing. NVSL and ARS staff are consulted as subject matter experts 

when necessary. 

Conclusion

The IAV voluntary surveillance system in swine continues to provide insight into the genetic makeup of 

circulating influenza A virus in limited populations of commercial pigs. Genetic information and virus 

isolates are made publicly available for further research and possible vaccine strain selection and efficacy 

testing. Influenza A virus in swine remains a dynamic virus with high levels of genetic variability in the 

hemagglutinin and neuraminidase genes. 

Table 6. Total number of subtyped isolates 

collected from 2009-present and available 

through the NVSL repository

 Subtype Number of isolates

H3N2 2,689

H3N1 25

H1N1 3,460

H1N2 3,160

Mixed 302

TOTAL 9,636
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2

Appendix 1. Regional Charts of HA and NA Combinations by Percentage

The following charts present the percentages of combinations of HA and NA by region based on ARS-NADC phylogenetic analyses. The results are 

reported from April 2021 through March 2022. These “heat maps” represent the percentage of combinations by using a color gradient where a 

deeper gradient color represents a greater percentage occurrence for a particular HA-NA combination. HA clusters are listed on the left vertical 

axis of the chart and NA clusters are listed on the bottom horizontal axis. Line up the HA cluster with the corresponding NA cluster to determine 

the occurrence of that particular combination. 
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2022, Quarter 2